Sorry if I treat you as if you know nothing here but if I assume you know what you are saying and you in fact misunderstood something, well we make no headroom. I deal with sailors all the time and we have to spell everything out. It's not the sailors fault, they are not trained to the level they one were.
If you have left the NAS on for a few hours and the HDD LED has not gone out, try the below steps.
1) After turning on the NAS let it sit for 10 minutes then unplug the Ethernet cable. Waiting another 1 minute does the HDD LED go out?
2) If it doesn't, reconnect the Ethernet cable.
3) Hopefully you have some shared folder on the NAS because now I want you to copy a LARGE file to it and watch to see if the LED goes out at all.
4) If the LED goes out then you have the LED wired improperly to the motherboard.
5) If the LED never goes out then shutdown the NAS, disconnect the hard drive cables, reboot (assuming you are booting from a USB drive).
6) Report what the HDD LED is doing from power on through bootup. If it is remains lit, either the HDD LED is connected tot he wrong location, or backwards, or your motherboard could just have failed.
7) If you remove the USB drive and power on the computer it should have nothing to boot from and the HDD LED should remain out.
If you could be as descriptive as possible it would help. And what version of FreeNAS are you running, I doubt it's the issue however you never know.
EDIT: So you are using the eSATA as well? You can try to unplug that one to see if the problem goes away.